DESCRIPTION: (Applicant's abstract) We propose to develop two general systems for whole genome analysis of Saccharomyces cerevisiae, which have been extensively feasibility tested, toward a goal of understanding the function of every gene and how the products of each gene operate in the context of all other gene products. First, we have developed a system, which we call molecular tagging, which allows large numbers of deletion strains to be analyzed in parallel. In this method, deletion strains are generated that contain unique 20 base tags that can be quantitatively detected by hybridization to an Affymetrix DNA chip which has already been developed and tested. We propose to use this method for functional analysis of the yeast genome by first creating tagged deletion strains for each open reading frame in the yeast genome. This collection of tagged deletion strains will be pooled and analyzed under different growth conditions. Strains with growth defects are depleted from the population and can be revealed by analyzing the molecular tags. To expedite the process of making the deletion strains we propose to synthesize the primers and generate the deletion cassettes that will be used to construct the deletions, and then send these to collaborating laboratories which will perform the transformations and initial analysis of the transformants. Second, we plan to construct a whole genome microarray by PCR amplifying each open reading frame in the yeast genome, and covalent coupling on a glass slide. This approach has been feasibility tested by fabricating microarrays containing one quarter of the yeast genome and monitoring gene expression recombination, and genetic diversity. These whole genome microarrays will be used to monitor changes in gene expression, evaluate DNA replication, recombination and determine messenger RNA stability and, generally to assign function-to the products of many of the open reading frames in the yeast genome. The large number of oligonucleotides required by both of these projects will be readily and cheaply prepared using newly developed 96-well oligonucleotides synthesizers which are already in production use.